this is needlessly pedantic

first, they are certainly not instructions so that is a much worse name

but more importantly, we use words in new contexts all the time. Do you object to calling the computer device "mouse" because it's not a mouse? how about "neural network"? "ignition" on an electric vehicle?

"cot" is no more misleading than thousands of words you use every day.

Anthropomorphizing is not pedantic, especially in a technical domain. I get the paper title and all, but at this point it's marketing.

They are instructions. Everything in the context is instructions for the next token. The "thought" guides the answer by providing clearer instructions.